7doc

Crystal structure of Zika NS2B-NS3 protease with compound 5

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Core protein

Zika virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Core protein × 1 （A0A142IX72） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （H8XX12） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2R4LVW1_ZIKV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–39； UniProt 1418–1456 Author chain G； PDBConstruct 1–39； UniProt 1418–1456

Core protein

Zika virus

UniProt A0A142IX72

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Core protein × 1 （A0A2R4LVW1） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Genome polyprotein × 1 （Q32ZE1） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Serine protease subunit NS2B × 1 （Q32ZE1） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A142IX72_ZIKV
Isoform	—
PDB entities	2, 4, 6
Chains and sequence ranges	Author chain B； PDBConstruct 1–153； UniProt 1513–1665 Author chain D； PDBConstruct 1–152； UniProt 1514–1665 Author chain F； PDBConstruct 1–158； UniProt 1510–1667

Genome polyprotein

Zika virus

UniProt Q32ZE1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
2	Protein heterocomplex	Heteromer	Protein 2	Core protein × 1 （A0A142IX72） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Core protein × 1 （A0A142IX72） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_ZIKV
Isoform	—
PDB entities	3, 5
Chains and sequence ranges	Author chain C； PDBConstruct 1–38； UniProt 1418–1455 Author chain E； PDBConstruct 1–39； UniProt 1419–1457

Genome polyprotein

Zika virus

UniProt H8XX12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
4	Protein heterocomplex	Heteromer	Protein 2	Core protein × 1 （A0A2R4LVW1） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H8XX12_ZIKV
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain H； PDBConstruct 1–153； UniProt 1514–1666

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7doc
Deposition date deposition_date	2020-12-14
Structure title title	Crystal structure of Zika NS2B-NS3 protease with compound 5
Keywords keywords	Viral protease, Protease inhibitor complex, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7doc__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7doc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7doc__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.69 Å
Rg (electron density)	15.48 Å
Total Rg	16.59 Å
Atom count	1372
Residues	192
Excluded volume	24226 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7doc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7doc__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7doc__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7doc__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`7doc__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Core protein
Molecular weight formula_weight	4347.7 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G
Atom count atom_count	5976

DMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVE

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Core protein
Molecular weight formula_weight	16342.6 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGK

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	4218.5 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13,2.1.1.56,2.1.1.57,2.7.7.48
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLV

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Core protein
Molecular weight formula_weight	16213.5 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

TTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGK

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Serine protease subunit NS2B
Molecular weight formula_weight	4361.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEE

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Core protein
Molecular weight formula_weight	16944.3 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

KKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKRE

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	16370.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

TTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKR

Source Source

Source organism organism	Zika virus
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	64320
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
Molecular weight formula_weight	810.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

XGKRK

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	371

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Unit-cell length a length_a	59.154 Å
Unit-cell length b length_b	59.614 Å
Unit-cell length c length_c	215.073 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.904 Å
Low-resolution limit resolution_low	45.630 Å
R factor r_factor	—
R_work r_work	0.2092
R_free r_free	0.2286

Crystal structure of Zika NS2B-NS3 protease with compound 5

1. Protein Identity and Related Structures Protein Identity & Related Structures

Core protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Core protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Genome polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Genome polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7doc__assembly_1__model_1

7doc__assembly_1__model_1 | I(q)

7doc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 water

7. Citations (1)